[Bioperl-l] Bio::Graphics::Panel can't locate object method 'start'...

[Matthew Vaughn]

Hello, all. First of all, let me introduce myself to the list as this 
is my first posting. I'm a postdoc in Rob Martienssen's lab at Cold 
Spring Harbor Lab where I work on a variety of plant genomic projects. 
I've been using BioPerl for about a year now and I find it absolutely 
invaluable.

Here's my problem: I just took the plunge and upgraded my BioPerl 
installation from 1.02 to 1.2 and I've run into a problem with 
Bio::Graphics that has broken many of my scripts. Essentially, it looks 
like elements of Bio::Graphics are calling methods that Bio::Seq 
doesn't have any more. I've condensed the problem into the following 
code snippet. It should produce a blank panel image, but instead dies 
with an error 'Can't locate object method "start" via package 
"Bio::Seq" at /Library/Perl/Bio/Graphics/Panel.pm line 45, <DATA> line 
141.'

Am I doing something dunder-headed or is this a real bug?

Thanks,

Matt Vaughn

#!/usr/bin/perl -w

use Bio::Graphics;
use Bio::SeqIO;

my $io = Bio::SeqIO->new(-file=>'testing.fa');
my $seq = $io->next_seq;
my $panel = Bio::Graphics::Panel->new(	-segment => $seq,
							-key_style => 'between',
							-pad_left  => 10,
							-pad_right  => 10,
							-width  => 800	);		
my $gd = $panel->gd;
print $gd->can('png') ? $gd->png : $gd->jpeg;